Hi DK, I didn't have the chance to look into this issue. John R, did you manage to figure out a solution? Thanks, John On 02/14/2016 07:54 PM, Koh, Daegene wrote:

Hi John,

Were you ever able to resolve this issue? I’m having the same problem on Comet.

Cheers, DK

...

On Nov 25, 2015, at 10:06 AM, John Regan wrote:

Hi All,

I recently moved to working on a new machine and I've run into problems with eps_writer and pyx and tex. It seems pyx and tex are not talking to one another. I know pyx can sometimes have an iffy relationship with tex but does anyone know how to make them like each other?

This is the output I get.

yt : [INFO ] 2015-11-25 14:51:23,198 xlim = 0.456408 0.541884 yt : [INFO ] 2015-11-25 14:51:23,198 ylim = 0.482775 0.568251 yt : [INFO ] 2015-11-25 14:51:23,200 Making a fixed resolution buffer of (('gas', 'H_number_density')) 800 by 800 Create Multiplot.... yt : [WARNING ] 2015-11-25 14:51:24,085 No field specified. Choosing first field (('gas', 'H2_fraction')) yt : [WARNING ] 2015-11-25 14:51:24,955 No field specified. Choosing first field (('gas', 'H_number_density')) still waiting for tex after 5 (of 60) seconds... still waiting for tex after 10 (of 60) seconds... still waiting for tex after 15 (of 60) seconds... still waiting for tex after 20 (of 60) seconds... still waiting for tex after 25 (of 60) seconds... still waiting for tex after 30 (of 60) seconds... still waiting for tex after 35 (of 60) seconds... still waiting for tex after 40 (of 60) seconds... still waiting for tex after 45 (of 60) seconds... still waiting for tex after 50 (of 60) seconds... still waiting for tex after 55 (of 60) seconds... the timeout of 60 seconds expired and tex did not respond. We try to finish the dvi due to an unhandled tex error still waiting for tex after 5 (of 60) seconds... still waiting for tex after 10 (of 60) seconds... still waiting for tex after 15 (of 60) seconds... still waiting for tex after 20 (of 60) seconds... still waiting for tex after 25 (of 60) seconds... still waiting for tex after 30 (of 60) seconds... still waiting for tex after 35 (of 60) seconds... still waiting for tex after 40 (of 60) seconds... still waiting for tex after 45 (of 60) seconds... still waiting for tex after 50 (of 60) seconds... still waiting for tex after 55 (of 60) seconds... the timeout of 60 seconds expired and tex did not respond. Traceback (most recent call last): File "OnAxisMultiPlot_TimeSeries.py", line 173, in <module> figsize=(8,4), shrink_cb=1.8) File "/cosma/home/jregan/YT/yt-x86_64/src/yt-hg/yt/visualization/eps_writer.py", line 1164, in multiplot bbox = (100.0 * d.canvas.bbox().left().t, File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py", line 156, in bbox obbox += cmd.bbox() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 181, in bbox self.finish() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 311, in finish self.doaxes() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 588, in doaxes self.dolayout() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 572, in dolayout self.doaxiscreate(axisname) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 248, in doaxiscreate self.axes[axisname].create() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 586, in create self.canvas = self.axis.create(self.data, self.positioner, self.graphtexrunner, self.errorname) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 245, in create return _regularaxis._create(self, data, positioner, graphtexrunner, self.parter, self.rater, errorname) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 146, in _create return layout(data) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 141, in layout self.painter.paint(canvas, data, self, positioner) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py", line 258, in paint _title.paint(self, canvas, data, axis, axispos) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py", line 109, in paint title = canvas.layer("title").text_pt(x, y, axis.title, titleattrs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py", line 334, in text_pt return self.insert(self.texrunner.text_pt(x, y, atext, *args)) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 1223, in text_pt return self.text(x * unit.t_pt, y * unit.t_pt, expr, *args, **kwargs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 1201, in text raise e pyx.text.TexResultError: TeX didn't respond as expected within the timeout period (60 seconds). The expression passed to TeX was: \scrollmode \raiseerror% \def\PyX{P\kern-.3em\lower.5ex\hbox{Y}\kern-.18em X}% \gdef\PyXBoxHAlign{0}% \newbox\PyXBox% \newbox\PyXBoxHAligned% \newdimen\PyXDimenHAlignLT% \newdimen\PyXDimenHAlignRT% \gdef\PyXFlushHAlign{0}% \def\PyXragged{% \leftskip=0pt plus \PyXFlushHAlign fil% \rightskip=0pt plus 1fil% \advance\rightskip0pt plus -\PyXFlushHAlign fil% \parfillskip=0pt% \pretolerance=9999% \tolerance=9999% \parindent=0pt% \hyphenpenalty=9999% \exhyphenpenalty=9999}% \newbox\PyXBoxVBox% \newdimen\PyXDimenVBox% \newbox\PyXBoxVAlign% \newdimen\PyXDimenVAlign% \newdimen\PyXDimenVShift% \long\def\ProcessPyXBox#1#2{% \setbox\PyXBox=\hbox{{#1}}% \PyXDimenHAlignLT=\PyXBoxHAlign\wd\PyXBox% \PyXDimenHAlignRT=\wd\PyXBox% \advance\PyXDimenHAlignRT by -\PyXDimenHAlignLT% \gdef\PyXBoxHAlign{0}% \immediate\write16{PyXBox:page=#2,lt=\the\PyXDimenHAlignLT,rt=\the\PyXDimenHAlignRT,ht=\the\ht\PyXBox,dp=\the\dp\PyXBox:}% \setbox\PyXBoxHAligned=\hbox{\kern-\PyXDimenHAlignLT\box\PyXBox}% \ht\PyXBoxHAligned0pt% {\count0=80\count1=121\count2=88\count3=#2\shipout\box\PyXBoxHAligned}}% \def\PyXInput#1{\immediate\write16{PyXInputMarker:executeid=#1:}}% \def\PyXMarker#1{\hskip0pt\special{PyX:marker #1}}%% \PyXInput{1}% After parsing the return message from TeX, the following was left: This is TeX, Version 3.14159265 (TeX Live 2015) (preloaded format=tex) Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 744, in _cleantmp texrunner.expectqueue.put_nowait(None) # do not expect any output anymore File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 148, in put_nowait return self.put(item, False) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 123, in put raise Full Full Error in sys.exitfunc: Traceback (most recent call last): File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 744, in _cleantmp texrunner.expectqueue.put_nowait(None) # do not expect any output anymore File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 148, in put_nowait return self.put(item, False) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 123, in put raise Full Queue.Full

The call I make is:

multi = eps.multiplot(NCOLS, NROWS, projections, bare_axes=True,cb_labels=colorbar_label, figsize=(8,4), shrink_cb=1.8)

Cheers, John

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

-- John Wise Assistant Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu

Hi John and DK, Sorry I only saw this late. For me the problem was also the texlive installation which I did eventually track down. The problem for me was not an older version however, simply that texlive wasn't installed on the compute nodes of the cluster I was using - it was however installed on the login nodes which I didn't cotton on to at first. This is likely to be a common problem with Pyx though when running (at least initially) on a new machine which won't usually have latex installed on the compute nodes. Something to be mindful of I think. On Tue, Feb 16, 2016 at 7:05 AM, John Wise wrote:

Hi everyone,

I just wanted to follow-up on this problem. I found that the latex version is very old (from 2007) on Comet. I installed my own version, using basic scheme with the TeX Live install script

http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz

and PyX works perfectly now without any errors or warnings.

Thanks, John

On 02/15/2016 01:51 PM, John Wise wrote:

...

Hi DK,

I didn't have the chance to look into this issue. John R, did you manage to figure out a solution?

Thanks, John

On 02/14/2016 07:54 PM, Koh, Daegene wrote:

...

Hi John,

Were you ever able to resolve this issue? I’m having the same problem on Comet.

Cheers, DK

On Nov 25, 2015, at 10:06 AM, John Regan

...

wrote:

Hi All,

I recently moved to working on a new machine and I've run into problems with eps_writer and pyx and tex. It seems pyx and tex are not talking to one another. I know pyx can sometimes have an iffy relationship with tex but does anyone know how to make them like each other?

This is the output I get.

yt : [INFO ] 2015-11-25 14:51:23,198 xlim = 0.456408 0.541884 yt : [INFO ] 2015-11-25 14:51:23,198 ylim = 0.482775 0.568251 yt : [INFO ] 2015-11-25 14:51:23,200 Making a fixed resolution buffer of (('gas', 'H_number_density')) 800 by 800 Create Multiplot.... yt : [WARNING ] 2015-11-25 14:51:24,085 No field specified. Choosing first field (('gas', 'H2_fraction')) yt : [WARNING ] 2015-11-25 14:51:24,955 No field specified. Choosing first field (('gas', 'H_number_density')) still waiting for tex after 5 (of 60) seconds... still waiting for tex after 10 (of 60) seconds... still waiting for tex after 15 (of 60) seconds... still waiting for tex after 20 (of 60) seconds... still waiting for tex after 25 (of 60) seconds... still waiting for tex after 30 (of 60) seconds... still waiting for tex after 35 (of 60) seconds... still waiting for tex after 40 (of 60) seconds... still waiting for tex after 45 (of 60) seconds... still waiting for tex after 50 (of 60) seconds... still waiting for tex after 55 (of 60) seconds... the timeout of 60 seconds expired and tex did not respond. We try to finish the dvi due to an unhandled tex error still waiting for tex after 5 (of 60) seconds... still waiting for tex after 10 (of 60) seconds... still waiting for tex after 15 (of 60) seconds... still waiting for tex after 20 (of 60) seconds... still waiting for tex after 25 (of 60) seconds... still waiting for tex after 30 (of 60) seconds... still waiting for tex after 35 (of 60) seconds... still waiting for tex after 40 (of 60) seconds... still waiting for tex after 45 (of 60) seconds... still waiting for tex after 50 (of 60) seconds... still waiting for tex after 55 (of 60) seconds... the timeout of 60 seconds expired and tex did not respond. Traceback (most recent call last): File "OnAxisMultiPlot_TimeSeries.py", line 173, in <module> figsize=(8,4), shrink_cb=1.8) File

"/cosma/home/jregan/YT/yt-x86_64/src/yt-hg/yt/visualization/eps_writer.py", line 1164, in multiplot bbox = (100.0 * d.canvas.bbox().left().t, File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py", line 156, in bbox obbox += cmd.bbox() File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 181, in bbox self.finish() File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 311, in finish self.doaxes() File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 588, in doaxes self.dolayout() File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 572, in dolayout self.doaxiscreate(axisname) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 248, in doaxiscreate self.axes[axisname].create() File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 586, in create self.canvas = self.axis.create(self.data, self.positioner, self.graphtexrunner, self.errorname) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 245, in create return _regularaxis._create(self, data, positioner, graphtexrunner, self.parter, self.rater, errorname) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 146, in _create return layout(data) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 141, in layout self.painter.paint(canvas, data, self, positioner) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py", line 258, in paint _title.paint(self, canvas, data, axis, axispos) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py", line 109, in paint title = canvas.layer("title").text_pt(x, y, axis.title, titleattrs) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py", line 334, in text_pt return self.insert(self.texrunner.text_pt(x, y, atext, *args)) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 1223, in text_pt return self.text(x * unit.t_pt, y * unit.t_pt, expr, *args, **kwargs) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 1201, in text raise e pyx.text.TexResultError: TeX didn't respond as expected within the timeout period (60 seconds). The expression passed to TeX was: \scrollmode \raiseerror% \def\PyX{P\kern-.3em\lower.5ex\hbox{Y}\kern-.18em X}% \gdef\PyXBoxHAlign{0}% \newbox\PyXBox% \newbox\PyXBoxHAligned% \newdimen\PyXDimenHAlignLT% \newdimen\PyXDimenHAlignRT% \gdef\PyXFlushHAlign{0}% \def\PyXragged{% \leftskip=0pt plus \PyXFlushHAlign fil% \rightskip=0pt plus 1fil% \advance\rightskip0pt plus -\PyXFlushHAlign fil% \parfillskip=0pt% \pretolerance=9999% \tolerance=9999% \parindent=0pt% \hyphenpenalty=9999% \exhyphenpenalty=9999}% \newbox\PyXBoxVBox% \newdimen\PyXDimenVBox% \newbox\PyXBoxVAlign% \newdimen\PyXDimenVAlign% \newdimen\PyXDimenVShift% \long\def\ProcessPyXBox#1#2{% \setbox\PyXBox=\hbox{{#1}}% \PyXDimenHAlignLT=\PyXBoxHAlign\wd\PyXBox% \PyXDimenHAlignRT=\wd\PyXBox% \advance\PyXDimenHAlignRT by -\PyXDimenHAlignLT% \gdef\PyXBoxHAlign{0}%

\immediate\write16{PyXBox:page=#2,lt=\the\PyXDimenHAlignLT,rt=\the\PyXDimenHAlignRT,ht=\the\ht\PyXBox,dp=\the\dp\PyXBox:}%

\setbox\PyXBoxHAligned=\hbox{\kern-\PyXDimenHAlignLT\box\PyXBox}% \ht\PyXBoxHAligned0pt%

{\count0=80\count1=121\count2=88\count3=#2\shipout\box\PyXBoxHAligned}}% \def\PyXInput#1{\immediate\write16{PyXInputMarker:executeid=#1:}}% \def\PyXMarker#1{\hskip0pt\special{PyX:marker #1}}%% \PyXInput{1}% After parsing the return message from TeX, the following was left: This is TeX, Version 3.14159265 (TeX Live 2015) (preloaded format=tex) Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 744, in _cleantmp texrunner.expectqueue.put_nowait(None) # do not expect any output anymore File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 148, in put_nowait return self.put(item, False) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 123, in put raise Full Full Error in sys.exitfunc: Traceback (most recent call last): File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File

"/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 744, in _cleantmp texrunner.expectqueue.put_nowait(None) # do not expect any output anymore File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 148, in put_nowait return self.put(item, False) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 123, in put raise Full Queue.Full

The call I make is:

multi = eps.multiplot(NCOLS, NROWS, projections, bare_axes=True,cb_labels=colorbar_label, figsize=(8,4), shrink_cb=1.8)

Cheers, John

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

-- John Wise Assistant Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org